Dock Sampling

Pose Sampling in DOCK

Don't get right DOCK pose? Well, this happens a lot... Docking is a complicated process, but it can be broken down to two main processes: scoring and sampling. This page is about sampling (in DOCK).

To investigate why you don't get the right DOCK pose (in the case you know the answer from a crystal structure), you can consider the following things:

1. Check if the bioactive conformation is sampled in docking. This is described here: http://wiki.uoft.bkslab.org/index.php/Screen3d
2. Dock the bioactive conformation rigidly. This is described here: http://wiki.uoft.bkslab.org/index.php/Multimol2db.py
3. Run scoreopt on the bioactive conformation to get a score for the crystallographic pose of your ligand. This is described here: http://wiki.uoft.bkslab.org/index.php/Scoreopt
4. Check if a bioactive orientation (or an orientation close to it is actually sampled in the docking process. This is what is described on this page.

Bioactive conformation sampled?

I want to make the following example: I predicted a fragment binding to the oxyanion hole, but when we determined the crystal structure, the fragment bound to the so-called distal site of AmpC (see picture on the right).